http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php CHARMM forums: minimization, normal modes, monte carlo CHARMM Forums - UBB.threads(tm) http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27850#Post27850 Posted by lennart:
Time is a foreign concept in MC, so any dynamical analysis would be indirect, eg via an energy surface constructed from your MC sample.]]> Tue, 05 Jul 2011 05:39:39 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27775#Post27775 Posted by lennart:
... ie, post a minimal input file giving the error and its output CHARMM version, installation options, compiler and hardware/OS are also helpful bits of information]]> Tue, 28 Jun 2011 03:34:39 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26955#Post26955 Posted by halx:
Hi, I want to look into a method to estimate entropies (for MM/PBSA) via normal mode analysis as described in Kongsted&Ryde, J Comput Aided Mol Des 2009, 23, 63. Basically a large protein is partitioned into a smaller subset of interest with a fi]]> Wed, 30 Mar 2011 06:33:11 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26800#Post26800 Posted by lennart:
OK. The information about the problem then is this: NUMBER OF SPECIFIED FREQUENCIES IS LESS THAN ONE (even though you specified something greater than 1) and the following was not recognized NFEQ 25 I think that NFEQ is simply not the correct]]> Thu, 17 Mar 2011 12:17:39 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26592#Post26592 Posted by rmv:
I suggest looking at the individual energy terms for more clues, maybe repeat with 'NPRINT 1' to get more detail. It is an unexpected result, even for the CONJ algorithm. Not enough detail posted to say much more. ]]> Mon, 21 Feb 2011 16:19:11 CST http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26391#Post26391 Posted by gianluca:
The MC manual says that "DMAX" is the initial maximum displacement of each instance in a group. Does this mean that the value specified by DMAX influences only the very first MC move? Thanks for your help!]]> Mon, 31 Jan 2011 00:12:30 CST http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26160#Post26160 Posted by allyd:
[quote=Ramya]Thank you so much Rick. I recompiled CHARMM with additional switches and now the MC trajectory is loaded in VMD. [/quote] Could you please share what those switches are?]]> Thu, 06 Jan 2011 11:01:43 CST http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=26088#Post26088 Posted by Ramya:
I tried MC simulation to perform conformational sampling of the pentapeptide. I used rigid translation and rotation for the water molecules and cart/tors for peptide. I ran for 90000 steps and when I clustered the trajectory, all were in single clust]]> Tue, 28 Dec 2010 03:04:44 CST http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=25823#Post25823 Posted by rmv:
If you are using an x86_64 Linux kernel, you may need to use the X86_64 keyword of install.com; this may be one issue that can cause a seg fault. You should run the test case suite for c35b1; if some of those scripts also produce seg faults, that']]> Sat, 20 Nov 2010 11:28:37 CST http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=25670#Post25670 Posted by JohnPenniston:
What are the alternate approaches you mention for determining the entropy of large systems, Rick? I'm trying to get the entropy on a very large system, and Vibran seems unable to handle it. John Penniston ]]> Sat, 23 Oct 2010 12:53:49 CDT